ord_explore test fixes

david-barnett · Nov 19, 2021 · 5bb846d · 5bb846d
1 parent 4f3152a
commit 5bb846d
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Showing 7 changed files with 47 additions and 54 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: microViz
 Title: Microbiome Data Analysis and Visualization
-Version: 0.8.0.9005
+Version: 0.8.0.9006
 Authors@R: 
     person(given = "David",
            family = "Barnett",

diff --git a/R/ord_explore.R b/R/ord_explore.R
@@ -628,7 +628,9 @@ ord_explore <- function(data,
       eventExpr = input$trans,
       handlerExpr = {
         x <- dist_choices(init$data, type = "all")
-        if (input$trans %in% trans_choices("log")) x <- x[x != "aitchison"]
+        if (input$trans %in% trans_choices("log")) {
+          x <- x[!x %in% c("aitchison", "jsd")]
+        }
         shiny::updateSelectizeInput(
           session = session, inputId = "dist", choices = x
         )
@@ -1136,11 +1138,10 @@ dist_choices <- function(data, type) {
     "va-wunifrac" = "va-wunifrac: variance-adjusted weighted UniFrac"
   )
   # add more phyloseq dist methods
-  pdists <- c(
-    phyloseq::distanceMethodList$vegdist,
-    phyloseq::distanceMethodList$betadiver,
-    phyloseq::distanceMethodList$DPCoA
-  )
+  pdists <- unlist(c(
+    "maximum", "binary",
+    phyloseq::distanceMethodList[c("vegdist", "betadiver", "DPCoA")]
+  ))
   more <- stats::setNames(object = pdists, nm = pdists)
   all <- c(all, more[!names(more) %in% names(all)])
 

diff --git a/tests/testthat/_snaps/ord_explore.md b/tests/testthat/_snaps/ord_explore.md
@@ -222,16 +222,16 @@
     Code
       dist_choices(esophagus, type = "tree")
     Output
-      gunifrac (Generalised UniFrac, alpha=0.5) 
-                                     "gunifrac" 
-                    wunifrac (weighted UniFrac) 
-                                     "wunifrac" 
-                   unifrac (unweighted UniFrac) 
-                                      "unifrac" 
-       va-wunifrac (variance adjusted weighted) 
-                                  "va-wunifrac" 
-                                          dpcoa 
-                                        "dpcoa" 
+             gunifrac: Generalised UniFrac, alpha=0.5 
+                                           "gunifrac" 
+                           wunifrac: weighted UniFrac 
+                                           "wunifrac" 
+                          unifrac: unweighted UniFrac 
+                                            "unifrac" 
+      va-wunifrac: variance-adjusted weighted UniFrac 
+                                        "va-wunifrac" 
+                                                dpcoa 
+                                              "dpcoa" 
 
 # ord_choices helper works
 

diff --git a/tests/testthat/_snaps/ord_explore/dietDistsAll.csv b/tests/testthat/_snaps/ord_explore/dietDistsAll.csv
@@ -1,9 +1,11 @@
 "","x"
-"none (for PCA/RDA/CCA)","none"
-"bray (Bray-Curtis)","bray"
-"aitchison (a.k.a. CLR & euclidean)","aitchison"
+"none: no distance used for PCA/RDA/CCA","none"
+"bray: Bray-Curtis","bray"
+"aitchison: CLR & Euclidean","aitchison"
 "euclidean","euclidean"
-"jsd","jsd"
+"jsd: Jensen-Shannon Divergence","jsd"
+"maximum","maximum"
+"binary","binary"
 "manhattan","manhattan"
 "canberra","canberra"
 "kulczynski","kulczynski"
@@ -41,7 +43,3 @@
 "sim","sim"
 "gl","gl"
 "z","z"
-"maximum","maximum"
-"binary","binary"
-"minkowski","minkowski"
-"ANY","ANY"
diff --git a/tests/testthat/_snaps/ord_explore/dietDistsNoTree.csv b/tests/testthat/_snaps/ord_explore/dietDistsNoTree.csv
@@ -1,9 +1,11 @@
 "","x"
-"none (for PCA/RDA/CCA)","none"
-"bray (Bray-Curtis)","bray"
-"aitchison (a.k.a. CLR & euclidean)","aitchison"
+"none: no distance used for PCA/RDA/CCA","none"
+"bray: Bray-Curtis","bray"
+"aitchison: CLR & Euclidean","aitchison"
 "euclidean","euclidean"
-"jsd","jsd"
+"jsd: Jensen-Shannon Divergence","jsd"
+"maximum","maximum"
+"binary","binary"
 "manhattan","manhattan"
 "canberra","canberra"
 "kulczynski","kulczynski"
@@ -41,7 +43,3 @@
 "sim","sim"
 "gl","gl"
 "z","z"
-"maximum","maximum"
-"binary","binary"
-"minkowski","minkowski"
-"ANY","ANY"
diff --git a/tests/testthat/_snaps/ord_explore/esoDistsAll.csv b/tests/testthat/_snaps/ord_explore/esoDistsAll.csv
@@ -1,14 +1,15 @@
 "","x"
-"none (for PCA/RDA/CCA)","none"
-"bray (Bray-Curtis)","bray"
-"aitchison (a.k.a. CLR & euclidean)","aitchison"
+"none: no distance used for PCA/RDA/CCA","none"
+"bray: Bray-Curtis","bray"
+"aitchison: CLR & Euclidean","aitchison"
 "euclidean","euclidean"
-"gunifrac (Generalised UniFrac, alpha=0.5)","gunifrac"
-"unifrac (unweighted UniFrac)","unifrac"
-"wunifrac (weighted UniFrac)","wunifrac"
-"va-wunifrac (variance adjusted weighted)","va-wunifrac"
-"dpcoa","dpcoa"
-"jsd","jsd"
+"jsd: Jensen-Shannon Divergence","jsd"
+"gunifrac: Generalised UniFrac, alpha=0.5","gunifrac"
+"unifrac: unweighted UniFrac","unifrac"
+"wunifrac: weighted UniFrac","wunifrac"
+"va-wunifrac: variance-adjusted weighted UniFrac","va-wunifrac"
+"maximum","maximum"
+"binary","binary"
 "manhattan","manhattan"
 "canberra","canberra"
 "kulczynski","kulczynski"
@@ -46,7 +47,4 @@
 "sim","sim"
 "gl","gl"
 "z","z"
-"maximum","maximum"
-"binary","binary"
-"minkowski","minkowski"
-"ANY","ANY"
+"dpcoa","dpcoa"
diff --git a/tests/testthat/_snaps/ord_explore/esoDistsNoTree.csv b/tests/testthat/_snaps/ord_explore/esoDistsNoTree.csv
@@ -1,9 +1,11 @@
 "","x"
-"none (for PCA/RDA/CCA)","none"
-"bray (Bray-Curtis)","bray"
-"aitchison (a.k.a. CLR & euclidean)","aitchison"
+"none: no distance used for PCA/RDA/CCA","none"
+"bray: Bray-Curtis","bray"
+"aitchison: CLR & Euclidean","aitchison"
 "euclidean","euclidean"
-"jsd","jsd"
+"jsd: Jensen-Shannon Divergence","jsd"
+"maximum","maximum"
+"binary","binary"
 "manhattan","manhattan"
 "canberra","canberra"
 "kulczynski","kulczynski"
@@ -41,7 +43,3 @@
 "sim","sim"
 "gl","gl"
 "z","z"
-"maximum","maximum"
-"binary","binary"
-"minkowski","minkowski"
-"ANY","ANY"